Copy Number

 

The putative cancer-associated GESPs driven by SCNAs in each cancer type were identified by four criteria: 1) located in a peak region of a significantly recurrent focal SNCA locus estimated by the genomic identification of significant targets in cancer (GISTIC2) algorithm, (q≤0.25); 2) altered with high frequency and large amplitude (G-score ≥0.1); 3) mRNA reliably detected in at least 10% of tumor specimens in the given cancer type (90th percentile of FPKM value ≥1); and 4) mRNA significantly and positively correlated with copy numbers (Pearson P-value less than 0.001).

 

Summary of the G-score of the putative cancer-causing GESPs driven by SCNAs in each cancer type


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ACCBLCABRCACESCCHOLCOADDLBCESCAGBMHNSCKICHKIRCKIRPLAMLLGGLIHCLUADLUSCMESOOVPAADPCPGPRADREADSARCSKCMSTADTGCTTHCATHYMUCECUCSUVM
 HGNC Name  Ensembl Gene ID  HGNC Symbol  Genomic Location  Amp  Del  Amp  Del  Amp  Del  Amp  Del  Amp  Del  Amp  Del  Amp  Del  Amp  Del  Amp  Del  Amp  Del  Amp  Del  Amp  Del  Amp  Del  Amp  Del  Amp  Del  Amp  Del  Amp  Del  Amp  Del  Amp  Del  Amp  Del  Amp  Del  Amp  Del  Amp  Del  Amp  Del  Amp  Del  Amp  Del  Amp  Del  Amp  Del  Amp  Del  Amp  Del  Amp  Del  Amp  Del  Amp  Del 
GTP binding protein overexpressed in skeletal muscleENSG00000164949GEMchr8:94249253-94262350:-                                                                                                                                                                                                  0.14                                                                0.39      
phospholipid phosphatase 5ENSG00000147535PPAPDC1Bchr8:38263130-38269243:-                                                                                                                                                                  0.11                                0.26                                                0.15                      
solute carrier family 26 member 1ENSG00000145217SLC26A1chr4:979073-993440:-                                                                                                                                                          0.42        0.1                                                                                                      
MET proto-oncogene, receptor tyrosine kinaseENSG00000105976METchr7:116672390-116798386:+                                                                                                  0.15                        0.18        0.19                                                                                                                                      
syndecan binding proteinENSG00000137575SDCBPchr8:58552924-58582860:+                                                                                                                                                                                                  0.13                        0.17                                        0.22      
carbonic anhydrase 9ENSG00000107159CA9chr9:35673856-35681159:+                                                                          0.3                                                                                        0.21                                                                                                      
ephrin A3ENSG00000143590EFNA3chr1:155078872-155087538:+                          0.2                                                                                                                                                                0.11                0.2                                                              
nicastrinENSG00000162736NCSTNchr1:160343272-160358952:+                                                          0.28                                                                                                                                0.11                                0.11                                              
proteolipid protein 2ENSG00000102007PLP2chrX:49171926-49175239:+                                                                                                                                                          0.49                                                                                                              
potassium voltage-gated channel subfamily E regulatory subunit 3ENSG00000175538KCNE3chr11:74454841-74467729:-                                                          0.49                                                                                                                                                                                                              
glycerophosphodiester phosphodiesterase domain containing 5ENSG00000158555GDPD5chr11:75434640-75525903:-                                                          0.49                                                                                                                                                                                                              
ATP binding cassette subfamily C member 4ENSG00000125257ABCC4chr13:95019829-95301446:-                  0.13                                                                                                        0.23        0.11                                                                                                                                      
rhomboid 5 homolog 2ENSG00000129667RHBDF2chr17:76470891-76501790:-                                                                                                                                          0.23                                                                0.25                                                              
solute carrier family 6 member 12ENSG00000111181SLC6A12chr12:190077-214570:-                                                                                                                                                          0.47                                                                                                              
podocalyxin likeENSG00000128567PODXLchr7:131500262-131558217:-                                                                                                                                                          0.46                                                                                                              
F11 receptorENSG00000158769F11Rchr1:160995211-161021348:-                                                          0.32                                                                                                                                0.14                                                                              
alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase BENSG00000167889MGAT5Bchr17:76868456-76950393:+                                                                                                                                                                                                  0.2        0.25                                                              
opsin 3ENSG00000054277OPN3chr1:241590102-241677376:-                  0.26                                                                                                        0.19                                                                                                                                              
ADAMTS like 4ENSG00000143382ADAMTSL4chr1:150549369-150560937:+                  0.45                                                                                                                                                                                                                                                      
ephrin B2ENSG00000125266EFNB2chr13:106489731-106535114:-                  0.13        0.2                                                                                                        0.12                                                                                                                                      

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